Reptiles in the ACT: where and when are they seen?

library(here)
library(galah)
library(skimr)
library(dplyr)
library(lubridate)
library(stringr)
library(ggplot2)
library(ggridges)
library(leaflet)
library(leaflet.extras)
library(reactable)
library(scico)
library(hrbrthemes)
library(patchwork)

reptilia <- readRDS(here("data", "reptilia"))

reptilia_tidy <- reptilia %>% 
  filter(cl22 == "Australian Capital Territory") %>% 
  rename(state = cl22, 
         forestType = cl10902) %>% 
  mutate(forestType = na_if(forestType, ""),
         family = na_if(family, ""),
         basisOfRecord = tolower(basisOfRecord),
         basisOfRecord = str_replace(basisOfRecord, "_", " "),
         eventDate = as_datetime(eventDate, tz = "Australia/Sydney", format = NULL),
         eventDate = as_date(eventDate, tz = NULL),
         month = month(eventDate))

Exploratory data analysis

Summary statistics

Summary statistics for fields in the dataset of reptile occurrences in the ACT

skim(reptilia_tidy)

Data summary

Name	reptilia_tidy
Number of rows	10145
Number of columns	12
_______________________
Column type frequency:
character	8
Date	1
numeric	3
________________________
Group variables	None

Variable type: character

skim_variable	n_missing	complete_rate	min	max	empty	n_unique	whitespace
scientificName	0	1	4	33	0	102	0
genus	0	1	0	16	106	52	0
family	38	1	8	15	0	11	0
order	0	1	0	10	4	3	0
dataResourceName	0	1	9	87	0	23	0
basisOfRecord	0	1	7	18	0	5	0
state	0	1	28	28	0	1	0
forestType	17	1	6	31	0	10	0

Variable type: Date

skim_variable	n_missing	complete_rate	min	max	median	n_unique
eventDate	5206	0.49	1954-01-22	2021-11-25	2012-10-08	1783

Variable type: numeric

skim_variable	n_missing	complete_rate	mean	sd	p0	p25	p50	p75	p100	hist
decimalLatitude	0	1.00	-35.34	0.15	-35.91	-35.40	-35.3	-35.24	-35.12	▁▁▃▇▇
decimalLongitude	0	1.00	149.11	0.30	148.76	148.99	149.1	149.15	150.77	▇▂▁▁▁
month	5206	0.49	7.92	3.92	1.00	3.00	10.0	11.00	12.00	▃▁▁▂▇

Occurrence map

Locations of reptiles in the ACT based on occurrence records of reptiles from the ALA. Interactive layers in the top right corner allow records to be differentiated based on the type of record (ALA id: basisOfRecord), forest type (ALA id: cl10902), and taxonomic family (ALA id: family) associated with each record.

Occurrence records

Occurrence records for reptiles in the ACT. Columns may be sorted by clicking on column names, or filtered using the search bars under each column header. A global search bar in the top right corner enables searching the whole table.

# remove cols not of interest in a table
reptilia_subset <- reptilia_tidy %>% 
  select(eventDate:basisOfRecord, forestType)

reactable(
  reptilia_subset,
  columns = list(
    eventDate = colDef(name = "Date"),
    scientificName = colDef(name = "Species"),
    genus = colDef(name = "Genus"),
    family = colDef(name = "Family"),
    order = colDef(name = "Order"),
    dataResourceName = colDef(name = "Source"),
    basisOfRecord = colDef(name = "Record type"),
    forestType = colDef(name = "Forest type")
  ),
  showSortable = TRUE,
  filterable = TRUE,
  searchable = TRUE,
  striped = TRUE
)

Occurrence records over time

All records

Reptile occurrence counts between 1954 and 2021 in the ACT

reptilia_tidy %>%
  filter(!is.na(eventDate)) %>% 
  group_by(eventDate) %>%
  summarise(count = n()) %>%
  ggplot() +
  geom_line(aes(x = eventDate, y = count), 
            color = "#41507B") +
  labs(x = "",
       y = "Count") +
  theme_ipsum()

Records by family

Reptile occurrence counts by taxonomic family between 1954 and 2021 in the ACT

reptilia_tidy %>%
  filter(!is.na(eventDate)) %>% 
  group_by(eventDate) %>%
  summarise(count = n(), family = family) %>%
  ggplot() +
  geom_line(aes(x = eventDate, y = count), 
            color = "#41507B") +
  facet_wrap(~family) +
  labs(x = "Date",
       y = "") +
  theme_ipsum()

Citation

ALA occurrence download https://doi.org/10.26197/ala.53fe1002-7e7f-48f5-bce7-7f1f503db4e2. Accessed from R with galah 1.3.1 (https://github.com/AtlasOfLivingAustralia/galah/) on 2021-12-04.

sessionInfo()

## R version 4.1.1 (2021-08-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19043)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
## [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
## [5] LC_TIME=English_Australia.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] patchwork_1.1.1      hrbrthemes_0.8.0     scico_1.2.0         
##  [4] reactable_0.2.3      leaflet.extras_1.0.0 leaflet_2.0.4.1     
##  [7] ggridges_0.5.3       ggplot2_3.3.5        stringr_1.4.0       
## [10] lubridate_1.7.10     dplyr_1.0.7          skimr_2.1.3         
## [13] galah_1.3.1          here_1.0.1          
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.4.2              tidyr_1.1.4             sass_0.4.0             
##  [4] jsonlite_1.7.2          bslib_0.3.1             assertthat_0.2.1       
##  [7] highr_0.9               triebeard_0.3.0         sp_1.4-5               
## [10] wellknown_0.7.4         urltools_1.7.3          yaml_2.2.1             
## [13] gdtools_0.2.3           Rttf2pt1_1.3.8          pillar_1.6.3           
## [16] lattice_0.20-44         glue_1.4.2              extrafontdb_1.0        
## [19] digest_0.6.28           leaflet.providers_1.9.0 colorspace_2.0-2       
## [22] htmltools_0.5.2         plyr_1.8.6              reactR_0.4.4           
## [25] pkgconfig_2.0.3         httpcode_0.3.0          purrr_0.3.4            
## [28] scales_1.1.1            tibble_3.1.5            proxy_0.4-26           
## [31] farver_2.1.0            generics_0.1.0          ellipsis_0.3.2         
## [34] withr_2.4.2             repr_1.1.3              magrittr_2.0.1         
## [37] crayon_1.4.1            evaluate_0.14           data.tree_1.0.0        
## [40] fansi_0.5.0             class_7.3-19            data.table_1.14.2      
## [43] tools_4.1.1             lifecycle_1.0.1         munsell_0.5.0          
## [46] compiler_4.1.1          jquerylib_0.1.4         e1071_1.7-9            
## [49] systemfonts_1.0.2       rlang_0.4.11            classInt_0.4-3         
## [52] units_0.7-2             grid_4.1.1              htmlwidgets_1.5.4      
## [55] crosstalk_1.1.1         labeling_0.4.2          base64enc_0.1-3        
## [58] rmarkdown_2.11          wk_0.5.0                gtable_0.3.0           
## [61] DBI_1.1.1               curl_4.3.2              R6_2.5.1               
## [64] knitr_1.36              fastmap_1.1.0           extrafont_0.17         
## [67] utf8_1.2.2              rprojroot_2.0.2         KernSmooth_2.23-20     
## [70] stringi_1.7.5           crul_1.1.0              Rcpp_1.0.7             
## [73] vctrs_0.3.8             sf_1.0-4                tidyselect_1.1.1       
## [76] xfun_0.26